{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["27(1)"],"submitter":["Matarrese MAG"],"funding":["European Union - NextGeneration EU - National Recovery and Resilience Plan (NRRP)","European Union – NextGeneration EU – National Recovery and Resilience Plan"],"pubmed_abstract":["The discovery of long non-coding RNAs (lncRNA) has revealed additional layers of gene-expression control. Specific interactions of lncRNAs with DNA, RNAs, and RNA-binding proteins enable regulation in both cytoplasmic and nuclear compartments; e.g. a conserved triple-helix motif is essential for MALAT1 stability and oncogenic activity. Here, we present a secondary-structure-based framework to annotate and detect RNA triple helices. First, we extend the dot-bracket formalism with a third annotation line that encodes Hoogsteen contacts. Second, we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones. Using telomerase RNAs and RNA-stability elements with experimentally established tri"],"journal":["Briefings in bioinformatics"],"pagination":["bbag009"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12834306"],"repository":["biostudies-literature"],"pubmed_title":["Decoding RNA triple helices: identification from sequence and secondary structure."],"pmcid":["PMC12834306"],"pubmed_authors":["Ballarino M","Luchetti N","Durante D","Matarrese MAG","Di Petta F","Tesei L","Chiodo L","Quadrini M"],"additional_accession":[]},"is_claimable":false,"name":"Decoding RNA triple helices: identification from sequence and secondary structure.","description":"The discovery of long non-coding RNAs (lncRNA) has revealed additional layers of gene-expression control. Specific interactions of lncRNAs with DNA, RNAs, and RNA-binding proteins enable regulation in both cytoplasmic and nuclear compartments; e.g. a conserved triple-helix motif is essential for MALAT1 stability and oncogenic activity. Here, we present a secondary-structure-based framework to annotate and detect RNA triple helices. First, we extend the dot-bracket formalism with a third annotation line that encodes Hoogsteen contacts. Second, we introduce TripleMatcher, which searches for a triple-helix pattern, filters candidates by C1'-C1' distance thresholds, and merges overlaps into region-level zones. Using telomerase RNAs and RNA-stability elements with experimentally established tri","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Jan","modification":"2026-06-15T08:49:17.998Z","creation":"2026-06-15T03:11:29.802Z"},"accession":"S-EPMC12834306","cross_references":{"pubmed":["41587321"],"doi":["10.1093/bib/bbag009"]}}